Software

 

The following programs were developed in the process of population genetic studies and projects at the Institute of Forest Genetics. For each program a short description is given and a download link is provided. The programs are distributed free of charge to academic users for research purposes. They are provided as is without warranty of any kind, including, but not limited to, fitness for a particular purpose, support or maintenance.

Eco-Gene 5.1
by Bernd Degen and Alexandre Sebbenn

For a comprehensive evaluation of human influences on the genetic system of tree populations, the simulation model ECO-GENE was developed. Eco-Gene implements simulations of temporal and spatial dynamics of genetic and demographic processes in tree populations. It is an individual distance-dependent tree model that combines elements of population genetic, demographic, forest growth and management models. Overlapping or discrete generations can be assumed and different processes, as for example, gene flow, mating system, flowering phenology, selection, random drift and intraspecific competition can be implemented. The model can be run with empirical and fictitious input data and takes up to 200 loci as input. The simulated genetic data can be directly analysed with established genetic analysis programmes.

Eco-Gene has been developed with the following tasks in mind:

• Analysis of complex population genetic interactions.
• Hypothesis testing of realized genetic systems in tree populations.
• Analysis of the effects of human influence on evolutionary processes in tree populations.
• Deduction of recommendations for sustainable management of genetic resources.

 Operating system: Microsoft Windows

For download click on the following link:
EcoGene.zip

Information on installation and usage of Eco-Gene can be found in the manual:
manual_Eco_Gene_5a.pdf

SpatialGeneticSoftware (SGS) 1.0d
by Bernd Degen

SpatialGeneticSoftware (SGS) provides a user friendly WINDOWS tool to analyse small and large scale genetic and phenotypic structures. The program can deal with nearly all types of genetic data such as codominant marker (allozyme, nuclear microsatellites), dominant marker (RAPDs, AFLPs) and uniparentally inherited markers (cp- and mt-haplotypes). Most of those data can be analysed on both scales, as individual genotypes of one population (small scale) and as frequencies of alleles or haplotypes for different populations (large scale). Furthermore, a simple approach to analyse the spatial structure of continuous quantitative traits is integrated.

The program offers various statistics to analyse the spatial genetic and phenotypic structure: Morans's index, Geary's index, number of alleles in common and approaches using genetic distances and Fst-values. The statistical significance of all measures is verified by use of permutation test. The results are visualized by different graphics that can be integrated via the clipboard to other Windows programmes. Furthermore, results are given in a table and can be stored as ASCII files.

Operating system: Microsoft Windows

For download click on the following links:
p_sgs.zip
sgs_exe.zip

Information on installation and the current update of SGS can be found here:
InstallationUpdateSGS.pdf

The manual of SGS can be downloaded here:
sgs_manual.pdf

FormatIn 1.2
by Jutta Buschbom

FormatIn is a Perl script that reads genotypic data as a tab-delimited table as well as in formats produced by several forest genetic simulation programs used in the modeling platform of the EU network Evoltree (e.g. VentouG, Metapop and Eco-Gene). It transforms the given data into the input formats required by commonly used population genetic programs: Arlequin, Cervus, FSTAT, GDA_NT, GenAlEx, GenePop, MLTR, POLDISP, SGS, SPAGeDi, Structure, and Swap.

The strength of FormatIn is that it captures population, family, and stage information and produces output taking into account this extra information according to user choice. The user can set output name, missing data value and choose if stage information should be taken into account to produce the output formats.

FormatIn will run on computers that have Perl installed. Information on where to get and how to install Perl, and how to use and run FormatIn can be found in the manual that is distributed with the script.

For download click on the following links:
FormatIn_12.zip (Windows)
FormatIn_12.tar.gz (Unix and Mac OS X)

Information on installation and usage of FormatIn can be found in the manual:
FormatIn12_Manual.pdf